Haunted by the past
by SuperMom1
Summary: John's in trouble again, but it isn't his fault. John and Rodney exploring an ancient lab, of course there's going to be trouble and some whump for a certain Colonel. Can be read on it's own, or It could be a prequel to the Pegasus series.
1. Chapter 1: Exploring Atlantis

**Disclaimer: I do not own Stargate or any of its characters. I do love to write about them though.**

**I've really wanted to write a John and Rodney story for a while, so when an idea popped into my head I thought I'd run with it. Set sometime in season three probably between the 'Return part two' and 'Sunday', but don't worry, I definitely will do at least one more story in my Pegasus series.**

**Chapter 1: Exploring Atlantis.**

John was not happy. How did he end up here? On their last ill-fated mission to explore ancient ruins, McKay had told him they were perfectly safe. Until the console, he was activating exploded in his face. Looking down at his bandaged hands, he realised that he had been lucky on that occasion to only receive minor shrapnel wounds to his hands. If he hadn't covered his face with his hands it could have been a lot worse. He swore that if Rodney ever said anything about an ancient ZPM lab again he was going to stun the man and take him to a holding cell.

He'd been in the infirmary for a couple of days, until he was begging Carson to let him out. He'd finally escaped the dodge, when McKay had tracked him down on his way to his quarters. Rodney had asked him to come and search for an ancient lab in the lower levels of the city. He was about to stun the man, when Rodney started to beg. It was a pitiful sight, but how could he refuse a begging McKay; after all Rodney was his best friend.

And that was what led him here; heading down a deep, dark, smelly, mouldy and damp corridor in the lower levels of Atlantis. His flashlight beam cast a narrow beam of light ahead of him. It was a bit depressing really. I'd rather be anywhere but here right now he thought.

"Why are we here?" John asked, with impatience in his voice.

"I think I've found ZPM storage room." Rodney told him, he was as excited as a little boy in a toy shop.

"We've been walking around down here for over an hour and we still haven't found anything. What makes you think you've found a storage room?" John asked becoming more impatient by the minute.

"I was looking through the ancient data base and it indicated that there was one here." Rodney's voice was high pitched with excitement.

"You do know that you can't trust everything the ancients say right? So it stands to reason that there may not be a lab down here." John explained.

"I'm willing to take that risk; you do remember that I ended up depleting the last ZPM sending the other me home to his universe." Rodney told him, still feeling extremely guilty about that event."

"How could I forget, Elizabeth was mad at you for a week?" John quipped.

"Yes well, she got over it eventually."

"Okay, you've explained why you're here, but why am I here?" John sighed.

"We're exploring, that's what we do remember and I might need your super gene for something." Rodney answered his voice dripping with sarcasm.

"Great I'm a human light switch," John grumbled more to himself than Rodney.

They walked on in silence for another ten minutes until McKay started to complain loudly.

"It really smells down here and it's really cold." He said shivering.

"_McKay! _ This was your idea and I was tempted to shoot you when you first suggested it. Keep quiet, because shooting you is still and option."

"Okay, but…," he never got to finish that sentence, as John pulled his stunner out and pointed it at him.

Sheppard lowered the weapon as his radio activated "Go ahead Elizabeth." He said tapping his earpiece.

"_How are things going down there John, have you found anything yet?" _

"Not really, this seems to be a complete waste of time." He told her, rolling his eyes.

"Elizabeth, are Ronan and Teyla back from the mainland yet? "John asked, before she had a chance to break the connection.

"_No not yet, we're not expecting them until this evening."_

"Okay let me know when they get back, Sheppard out."

"_Will do, stay safe and report in an hour, Weir out."_

John continued to walk down the dark mouldy, damp corridor with Rodney following behind.

"Have you found anything yet McKay?"

"There's some interesting mould growing on the walls. Katie Brown would be interested in collecting a sample of that."

"Why are you suddenly so interested in mould McKay, or is it you're interested in a certain botanist?"

"I'm not sure what she really thinks of me Sheppard, but I'm certainly interested in her, I'm thinking of taking her on a date to…."

"Okay McKay, enough of your love life, I really don't want to know." John interrupted.

"Okay," was all that Rodney said, as they continued on in silence.

John was really starting to get annoyed at this point; he had better things to do. He had a huge mound of paperwork sitting on his desk; even that looked much more exciting than this did. John walked on for another five minutes. He was watching Rodney, who was talking to himself, as he looked at his tablet.

"_McKay!"_ He drawled with annoyance in his voice.

"Hang on I think I've found something." Rodney told him holding his fist up in the air.

"_Well!_ Have you found something or not McKay?" He replied ready to erupt.

"Yes, yes, yes, there's a door up ahead."

"Wow a door." John replied sarcastically, rolling his eyes.

"Oh Har, Har," Rodney replied glaring at him.

Rodney tried to open the door and it wouldn't open. He looked down at his tablet and a typed a few sentences, before looking at John.

"Sheppard can you open this door?"

Sheppard just showed him his bandaged hands and quipped, "Not with my hands."

"How about, just thinking about it, Sheppard?" He replied impatiently.

Sheppard closed his eyes a thought open and then all of a sudden there was a scraping sound as the door began to open.

**XXXXXXXXXXXXX**

Elizabeth sighed, as she looked at the reports on her desk. It was evaluation time and her senior staff had handed her the evaluations on all their staff members. Why did they make her job so difficult? Sheppard gave everyone an above average or excellent and then insisted that everyone who worked for him was above average or excellent. Rodney just refused to do it telling her it was a waste of time, unless she wanted him to point out everyone that was incompetent, that was much easier he told her. She was deep in thought when a Scottish voice startled her.

"Hi Lassie ya look deep in thought?"

She looked up to see Dr Carson Beckett walking into her office.

"Oh, hi Carson, how are you, what can I do for you?"

"Aye I'm fine Lassie, but feeling a wee bit annoyed with Colonel Sheppard."

"Okay Carson what's John done now?"

"He was due in the infirmary thirty minutes ago for a check-up on his hands."

"He's off exploring with Rodney. I'll radio him and let him know you're after him."

"He'd better get up to my infirmary as soon as possible, or next time I see him I'll sedate him and keep him there." Carson was quite annoyed when he'd finished his rant.

Elizabeth tapped her radio and called Sheppard, "John, are you there?"

"_Go ahead Elizabeth."_

"Carson's after you. You missed your check-up."

"_Aw crap is he mad at me?"_

Elizabeth smiled before she answered. "His exact words were he'd better get up to my infirmary as soon as possible, or next time I see him I'll sedate him and keep him there."

"_Is Carson there"_ he asked.

"Ay I'm here Colonel; I'll see you in thirty minutes."

"_I'll be there when we've explored this lab."_ John stated firmly.

"You'd better be Colonel or I _will_ sedate you!" Carson told him.

"_Okay we've just found a lab and were going in, Sheppard out."_

"Okay be careful, Weir out."

"Why do I have a bad feeling about this?" Carson asked her.

"It's Rodney and John, in an ancient lab. That usually spells trouble." She sighed.

"Okay I'm heading back to the infirmary. I'll see you later." Carson told her as he left her office.

Elizabeth just looked at her computer, not really able to concentrate any longer. She was worried about Rodney and John as always.

**XXXXXXXXXXXXX**

John pushed on the door and it opened, the lights came on automatically, as they entered the lab. They looked around and what they saw were ZPM's as far as the eye could see. Most were depleted, but there were few that were fully charged.

Rodney almost wet his pants in excitement and he yelled out. "Do you see what I see Sheppard Zed PM's!"

"Lots and lots of ZPM's" Sheppard replied.

Sheppard tapped his radio and spoke, "Elizabeth, we've found some kind of ZPM storage lab, we're just going to explore for a while and then we'll finish up and head back."

"_Okay, keep in touch Elizabeth out."_

"See you soon, Sheppard out."

It was a large room with shelf after shelf of ZPM's. They continued to search in silence for a while before Sheppard spoke.

"Why do you think they needed all of these ZPM's?"

"Maybe they actually manufactured them on Atlantis and shipped them off to all their bases throughout the galaxy." Rodney told him, his excitement building again.

"So that would mean…" John started, before Rodney interrupted.

"That the equipment to make Zed PM's and hopefully to recharge them is right here on Atlantis.

"Cool," was all that Sheppard could say.

"Maybe there's another lab that the equipment is in." Rodney told him, while bouncing on his toes.

They began to look around the room for another lab, in which the technology might be located. They looked around for another five minutes before Sheppard called out.

"There's a secret door over here."

Rodney, practically ran to the over side of the room.

"Gee, McKay that's the fastest I've ever seen you run." Sheppard quipped.

"Thanks I think. Now can you open this door or not?" Rodney asked him impatiently.

Sheppard thought open and the door opened. As they entered the lab the lights came on automatically, just like before.

They looked around and saw all kinds of interesting machinery.

"I wonder what all of these do?" Sheppard asked curiously.

"Let's see if we can find out. There's a computer console over in the corner of the room." McKay told him.

The walked cautiously over to the console. Rodney waved his hand over it and nothing happened.

"Why am I not surprised?" He muttered.

Sheppard looked at the console and noticed that it had grooves to place a person's fingertips on; luckily his fingertips weren't bandaged. With hesitation he put the fingertips of his right hand on the panel, nothing happened initially, but then a steady hum started up and all of a sudden he was enveloped by a blue light.

"Aw crap," he muttered.

A second blue light scanned Rodney a few seconds later, and then a hologram appeared in front of them and spoke. "Unknown DNA detected, the ZPM Lab is compromised and must be destroyed, two minute countdown initiated."

The door to the inner lab was locked and the hologram continued to speak, the blue light continued to envelope Sheppard.

What she said next shocked them the most.

"Tobias Sheppard has been detected in this lab; he must be restrained and punished for his crimes."

All of a sudden Sheppard went rigged and a needle was injected into his arm, his eyes rolled into the back of his head and he collapsed.

Rodney rushed over to Sheppard's side and tried to check his pulse, but he couldn't touch him as Sheppard was restrained by an invisible force field.

Sheppard let out a long deep groan as his muscles began to twitch and convulse. Then as suddenly as the groaning and twitching had started it stopped.

Rodney looked at the hologram and told her. "That is John Sheppard, not Tobias Sheppard; you've got the wrong man."

"His sentence has already been decided." The hologram told him.

"What's going to happen to him?" Rodney asked in full blown panic mode.

"He has been injected with a drug that will slowly decrease his body functions. We are not heartless; he will die a slow peaceful death."

"Is there any way to reverse the effects of the drug?" Rodney asked, trying to calm his frazzled nerves.

"There is an antidote, if the ruling council sees fit, he will be released from the force field and the antidote administered.

"This is not good." Rodney muttered.

Looking around the lab he tried to assess the situation. This hologram was really beginning to annoy him; he wished he could switch it off.

Suddenly a loud thunderous noise came from the outer lab. Instinctually, he covered his ears and protected his head, as an explosion ripped through the outer lab. Luckily the room they were in seemed to be shielded.

As the explosion in the outer room settled, he looked around and realised that the hologram had disappeared, but the force field holding Sheppard was still intact.

Rodney tapped his earpiece. "Elizabeth we have a big problem."

**TBC…**

**Please review and let me know what you think.**


	2. Chapter 2: Who is Tobias Sheppard?

**Chapter 2: Who is Tobias Sheppard?**

Elizabeth was sipping her coffee and rubbing her temples, her head was really beginning to hurt. She'd just given Teyla and Ronan permission to stay with the Athosians on the mainland overnight when Carson entered her office.

She sighed and asked, "Don't tell me, John hasn't showed up in your infirmary?"

"No and I can't seem to contact him on the radio either." He replied.

Elizabeth tapped her radio. "John, can you hear me?" she waited a few minutes and no reply.

Carson tapped his earpiece and tried again. "John can you hear me?"

There was still no reply.

Carson looked at Elizabeth and asked, "Do you know where they were heading?"

"No not really, they were just exploring some ancient lab."

"I have a very bad feeling about this," Carson said in a worried tone.

Elizabeth tapped her earpiece "Dr Zelenka, Major Lorne please report to my office immediately?"

"_I'm on my way." _Lorne replied sensing the urgency in her voice.

"_I'll be there in a few minutes."_ Zelenka told her.

Elizabeth just sat there continuing to rub her aching temples. Carson handed her some Tylenol, she smiled at him and took them.

"What now?" Carson asked her.

"Now we wait."

**XXXXXXXXXXXXX**

_Rodney tapped his earpiece. "Elizabeth we have a big problem." _There was no reply.

"Elizabeth come in this is Rodney?"

"Zelenka, Lorne do you read me? This is Rodney."

Still no reply, "okay communications must be down, that's the first thing I need to fix." He muttered to himself.

A moan came from the other side of the room, as Sheppard started to wake.

"How do you feel John?" Rodney asked.

"Like…crap." John rasped out, while taking deep shallow breaths.

"Wha…appened?" John slurred out.

Rodney looked at him. "This is going to be difficult to explain."

"Try," was all the John could manage to say.

"Well the computer scanned me and detected, unknown DNA."

John looked at him with a strange look on his face.

"I know weird right?" McKay said and shrugged.

"McKay what happened to me?" John asked a little more coherent this time.

"Well when it detected your DNA, it mistook you for someone named Tobias Sheppard."

"Who the hell is Tobias Sheppard?" John asked; he had a bad feeling about this.

"I don't know, but it seems he was some kind of criminal, who the ancients were looking for." Rodney told him looking in the opposite direction.

"What is going to happen to me?" Sheppard asked, looking worried.

"Ummm."

"_McKay! _I want to know the truth?" John pleaded.

"Well it seems that you have been sentenced for Tobias' crimes." Rodney told him, trying to remain calm.

"And?"

"You've been injected with a drug which will slowly shut your body down and you will die, the hologram said that it shouldn't be too painful and you will die peacefully."

"I don't plan on dying at all, is Carson is on his way? John asked.

"No, an explosion has destroyed the outer lab and communications are down."

"Could this get any worse?" John asked.

"Well…, even if Carson could get in here, you're trapped in a force field, that I can't get you out of."

"Well McKay you'd better get to work then, hadn't you?"

At that moment Sheppard yelled out as his body began to convulse. "I though this wasn't supposed to be painful."

"Something must have gone wrong."

"Ya think?" Sheppard said through gritted teeth as his body continued to convulse.

After what seemed like hours the convulsions ceased and he lost consciousness.

**XXXXXXXXXXXX**

Elizabeth and Carson were becoming anxious by the time Lorne and Zelenka entered her office. They had been trying to raise John or Rodney for almost ten minutes and still there was no reply.

As the two men sat down Elizabeth spoke, "Gentlemen we have a situation, we have lost contact with Colonel Sheppard and Doctor McKay. The last time I spoke to John via the radio, they had discovered an Ancient lab, which may have been a ZPM storage room. They were heading into investigate. That was and hour ago."

"Dr Zelenka, do you know what area they were exploring?" She asked the scientist.

"Yes I have a fair Idea what direction they were heading in."

"Okay, give Major Lorne directions, and then I want you to try and work out a way to communicate with them?" Elizabeth told him.

"Yes Ma'am," Zelenka replied.

"Lorne can you start a search? Teyla and Ronan will join you shortly. I've called them back form the mainland and filled them in on the situation."

"Yes Ma'am." Lorne replied.

"I'm going with Major Lorne," Carson told them. "It's Colonel Sheppard and Dr McKay, there probably in trouble and in need of a doctor."

"Okay as soon a Ronan and Teyla arrive, you can start your search. You're dismissed." Elizabeth said the worry evident in her voice.

Just then Ronan and Teyla entered the room. "We are here, when can we begin the search?" Teyla asked.

"Right away," Lorne told them.

"I'm ready, let's get going?" Ronan grunted.

They left Elizabeth's office, not knowing what they were going to find or whether it would be too late to help their friends. Rodney and John were in trouble they knew it. John Sheppard was a trouble magnet when he was on his own, but put Rodney McKay into the picture and the chances of them getting into trouble were ten times worse; especially when it came to investigating ancient technology.

**XXXXXXXXXXXXX**

John struggled with the darkness that surrounded him, he knew he was in pain, but he couldn't work out why. A presence came to him in the darkness and he couldn't work out whether he was imaging things or not, but then it spoke.

"Tobias, you have been sentenced and punished for collaborating with our enemy."

"What?" John asked the voice

"You were collaborating with the wraith. This act has led to death of a countless number of our people."

"That wasn't me; it must have been my ancestor." John told the voice.

"DNA doesn't lie. You will die for your treason, but it will be a peaceful death for you."

The voice disappeared and John was left all alone in the pain and darkness. This didn't feel very peaceful to him. He lay there thinking about his fate, as awareness slowly left him.

**XXXXXXXXXXXXX**

Rodney was looking around the lab for a communications console or any way to escape, when Sheppard started to mutter, "I'm not him, I'm not Tobias."

Rodney went over to see him and saw that he was still unconscious.

"As soon as we get out of here, I'm going to have to find out who this Tobias Sheppard is." Rodney muttered.

He continued to look around and saw nothing. This was becoming extremely frustrating for him.

"Okay, so Com's are not working, is there a way I can disable the force field around Sheppard." He mumbled, to himself.

He looked around the lab again looking for a force field emitter this time.

Rodney worked on, all the while mumbling to himself. He checked on Sheppard from time to time, when he heard him mumbling or moaning in pain.

"Okay I need to find out what the antidote is, once I've disconnected the forcefield." Rodney continued to mutter, making a list of priorities.

Suddenly John yelled out in pain and went ridged, he appeared to stop breathing. Rodney held his breath and then John started breathing again; he let out a sigh of relief. John was pale and sweat was forming on his brow. He looked to be in incredible pain; so much for not being painful

"This is very bad." Rodney muttered to himself

**XXXXXXXXXXXXX**

Zelenka rushed into the lab that he shared with McKay. He had one thought on his mind he must find a way to communicate with Rodney. Sitting down at his computer he realised that they had a problem.

"Dr Weir, this is Radek. We have a big problem in the lower levels."

"_What seems to be the problem Dr Zelenka?"_

"I have some good news and bad news."

"_Okay Radek what's the good news?"_

"The good news is I know exactly where they are, the bad news is there has been an explosion in that section and I don't know if the area is structurally sound or not."

"_Okay, send me Lorne the Coordinates and keep working on a way to contact them, Weir out."_

"Okay, will do, Zelenka out."

Radek went over to the coffee pot to pour himself a cup of coffee; he looked inside and saw only dregs. "I better fill this up," he muttered. "I think it's going to be a long night."

**XXXXXXXXXXXXX**

Lorne was heading down a dark corridor with Teyla, Ronan and Carson behind him when his radio activated.

He tapped his earpiece to find Dr Zelenka on the other end. "What have you go Doc?"

"_I'm sending you the possible location of Dr McKay and Colonel Sheppard, but it looks as if there has been an explosion in that area recently."_

"Okay thanks Dr Zelenka, Lorne out."

"_I'm still trying to find a way to communicate with them, Zelenka out."_

"Major Lorne what is happening?" Teyla asked.

"Dr Zelenka has found out where they are, but there has been an explosion in that section. He's not sure how structurally sound it is down there." Lorne told her.

"Okay let's go then," Ronan grumbled.

"It's not as simple as that Ronan I need to contact Dr Weir and get a team of combat engineers down here to make sure it is safe. The last thing we need is to make it worse for Colonel Sheppard and Dr McKay." Lorne told him.

"Aye I agree. If there's been an explosion chances are that at least one of them is injured and the last thing we want is to injure them further." Carson explained to them.

Lorne tapped his radio, "Dr Weir, its Major Lorne."

"_Ah Major I was just about to contact you, did you get the coordinates from Dr Zelenka?"_

"Yes we did, how shall we proceed knowing that there's been an explosion?"

"_I'm sending a team of combat engineers to you now; wait for them before you precede any further, Weir out."_

"Okay, we'll stay here and wait, Lorne out."

He looked at the others and told them, "Okay, take a break for a few minutes while we wait for the combat engineers."

They sat next to the wall looking around at the damp place they were in. It was really disgusting and they hoped that they wouldn't have to stay there long. They sat there in silence with their own thoughts, thinking about all the times that John and Rodney had been in similar situations.

Teyla thought back to the last mission they had been on. It was just supposed to be a quick trip to investigate an ancient lab, but of course things were never that simple. A console had exploded and John had ended up in the infirmary for two days. One of which he was completely unconscious and unresponsive. Luckily the injuries to his hands weren't too serious, but they were bad enough to keep John in the infirmary for two days. This kind of thing happened far too often when John and Rodney were together. It had to stop, she thought to herself.

**XXXXXXXXXXXXX**

John was slowly coming to awareness again. The pain in his body continued to escalate, his muscles were hit by constant tremors, his head was beginning to pound and he was certain he had a fever. He tried really hard to open his eyes, but they just didn't want to open. Eventually he managed the feat and looked around the lab.

"Rodney… Why… Is…it….so….dark….in….here? He stammered in between shallow breaths.

Rodney looked around the lab confused before telling him, "The lights are still on Sheppard."

Despite his pain and grogginess, Sheppard started to panic. "Rodney…, what's… happening to me? I…Can't…see…."

Rodney knelt next to his friend and looked into his eyes, what he saw shocked him; there was cloudy film over his pupils. No wonder he couldn't see.

"John, listen to me you're going to be okay, I've found the forcefield emitter and I think I can disable it. When that's done I'm going to find a way to contact Elizabeth, so that someone can come and get us out of here. You'll be in the infirmary in no time. You just have to hang on."

"Usually…I'm...the…optimistic…one," John stammered.

"Well just rest and before you know it Carson will be here."

"Thanks…Rodney." He rasped out as a sudden spike of pain hit him and he lost consciousness again.

Rodney looked over at the force field emitter and then looked down at his stunner. What have I got to lose he thought.

"I think I'll take a leaf out of Conan's book," he told himself as he pulled out his stunner and shot the emitter.

The emitter crystals sent out a shower of sparks, as the stunners beam hit them. Rodney had to cover his face to protect it.

When the sparks had finally settled, he looked over at Sheppard and realised that it had worked.

"It worked," he said to himself.

He walked over to Sheppard and knelt beside him; grabbing his wrist he took his pulse.

"Not good." He muttered. "Okay Sheppard one job down, now I have to find a way to get us out of here and then once your safe in Carson's Clutches, I need to work out who the hell Tobias Sheppard was and what was his crime against the ancients, but the first thing we need to do when we get out of here is find an antidote."

There was no reply, as Sheppard was unconscious.

**XXXXXXXXXXXXX**

Finally the team of Combat engineers joined up with Lorne and the others. They were glad to see them as it meant that they could continue their search.

"Major, I'm sorry it took so long. We needed to get our gear organised." Harris told him.

It was Ronan who spoke next, "Can we get going?"

"Okay Ronan, I'll lead the way and you take our sixth." Lorne told him.

They continued to walk down the corridor until they came to a junction; Lorne took a left and continued on. There was smoke in the air indicating that they must have been getting close.

They continued on for another five hundred metres and then they saw it, the aftermath of the explosion, there was twisted metal and shattered glass. There was burnt out wiring and rubble piled high in the middle of the path.

Crap, this is going to take a while Lorne thought to himself.

Ronan just headed straight up to the mess and started lifting rubble out of the way.

"Ronan wait until we assess the structural integrity of the area." Harris told him.

"They may not have time to wait," Ronan growled at him.

"Ronan we must wait, as we do not want to risk injuring them further." Teyla soothed.

At that moment the wall started to shudder and dust began to fly.

"Run" Lorne yelled out.

They all ran until they were a safe distance away. When they looked back they realised that there was more rubble blocking there path.

Lorne tapped his earpiece. "Elizabeth we have a big problem."

**TBC…**

**I hope you still like it. Please review.**


	3. Chapter 3: A very sick Colonel

**Disclaimer: I am not a Doctor or medical health care professional. Although I have tried to research medical terms, they may not be 100 percent accurate.**

**Chapter 3: A Very sick Colonel.**

Elizabeth had no idea how long it had been since she'd left her office to take a break, but it seemed like days.

It had been over an hour since Lorne left her office to search the lower levels and she still hadn't heard from him; other to request a team of combat engineers. Zelenka left about the same time and all she'd heard from him was that there had been an explosion in the vicinity of John and Rodney's location. She sighed and looked down at her coffee cup. Empty again she thought.

Getting up to stretch her legs she wondered over to the coffee pot and found it empty.

"How many cups have I had today?" She mumbled.

Wandering back to her desk, she sighed again thinking of Rodney and John, wondering what kind of mess they had gotten themselves into this time.

She settled in to her chair just as her radio activated.

"_Elizabeth we have a big problem."_

"What's the problem Major Lorne?"

"_The path to the lab Sheppard and McKay a trapped in is completely blocked."_

"What are you thinking Major?"

"_I suggest we try and find another way into the lab. We'll keep working here, but Zelenka needs to find another way into that lab."_

"Okay I'll let him know, Elizabeth out."

"_I'll contact you soon, Lorne out."_

She sighed again, for the hundredth time that day. What now? She thought to herself, as her radio activated again.

"_Dr Weir, this is Dr Zelenka."_

"Go ahead Doctor."

"_I've found a way to contact the Colonel and Dr McKay. I've just got to finish a few things off and then you should be able to contact them."_

"Thankyou Doctor, once you've finished that can you start looking for another way into that lab; the passageway Lorne has found is completely blocked by a roof fall. They are trying to dig them out, but it will take hours.

"_Okay I'm on it, Zelenka out."_

"Keep me appraised, Weir out."

"Could this get any worse," she asked herself. They'd had way too many close calls over the years since they had entered the Pegasus galaxy. She turned her head heavenward and prayed that this wouldn't be another one.

**XXXXXXXXXXXXX**

Rodney was exploring every inch of the lab looking for another exit, when his radio activated.

"Elizabeth you don't know how good it is to hear you voice?" He told her with a sense of relief flooding him.

"_What's the situation Rodney?"_

"Well let's see where do I start? A megalomaniac hologram has mistaken Colonel Sheppard for someone called Tobias Sheppard and sentenced him to death, there was an explosion in the ZedPM lab and we can't find any way out of here. I think that just about covers it." Rodney said with anguish in his voice.

"_Rodney, slow down a bit, what do you mean the John has been sentenced to death?"_

"It seems that this Tobias Sheppard; I'm assuming that he is an ancestor of John's, was accused of a crime and has been found guilty, his sentence has been decided and is now being carried out. Only they've got the wrong man.

"_Rodney Calm down and tell me what has happened to him?"_

"He was injected with a drug that is designed to slowly shut down his body. Apparently it isn't supposed to be painful, but he is in a lot of pain; oh and he's also blind. There is an antidote, but I need to get out of here to find it. Elizabeth you really need to get Carson in here as soon as possible, because he's dying and I don't know how much longer he has."

"_Stay calm Rodney we're working as quickly as possible, Weir out."_

"Well work faster, Rodney out."

Rodney went and knelt beside his friend "I'm sorry Sheppard, I never meant for any of this to happen."

"Not…you're…fault." John stammered before moaning in pain.

"Try to rest John, I just spoke to Elizabeth and they're working on getting us out of here."

"So….hot…,why …is …it…so… hot…in…here?"

"I think you have a fever John, I'll find you a drink of water and try to cool you down."

"Kay," John replied before closing his eyes.

Rodney managed to find a canteen of water and start sponging his friend down. He thought how much he'd changed over the last three years and how John had played a big part in his transformation, by just accepting him for who he was. With a determined look in his face he looked down at his best friend and vowed that he was going to get him out of there no matter what.

**XXXXXXXXXXXXX**

Carson heard the whole exchange between Rodney and Elizabeth and knew that he had to do something soon or the Colonel wouldn't make it.

Tapping his earpiece he contacted Rodney, "Rodney its Carson, what's John's condition?"

"_I've just taken his temperature and its 105, he can't see and he keeps having muscle tremors and convulsions."_

"How long have the convulsions been going on Rodney?"

"_How long have we been in here, because that's about how long, they've been going on."_

"Okay you're going to have to keep him as cool as possible. Take his top off and keep sponging him down with as much water as you can spare."

"_Okay, but what about getting out of here?"_

"Zelenka is working on that, _you _need to focus on keeping him alive."

"_Okay Carson, just be quick, McKay out."_

"Aye will do lad, Carson out."

Carson turned to look at what the combat engineers were doing and found that they really hadn't moved much rubble.

"Major Lorne, how much longer do you think this is going to take?" Carson asked with frustration and worry in his voice.

"I'm sorry, but it's going to take hours." Lorne told him.

"The Colonel may not have hours." He told Lorne,

"Okay, how can we get to him?" Carson mumbled to himself.

Tapping his earpiece he called Zelenka, "Carson to Zelenka, come in please?"

"_How can I help you Carson?" Zelenka asked him._

"We need to get into that lab in a hurry; I don't think that Colonel Sheppard has much time."

"_I haven't found another way in yet Carson, but I'm working as quickly as I can."_

"Could we cut through the floor above them?"

"_I don't know Carson, but I will check it out and get back to you, Zelenka out."_

"Okay keep me informed, Carson out."

He sat down with his back against the wall and had a drink of water and took some Tylenol; for his ever increasing headache. He was totally frustrated, he had a patient that was in desperate need of medical attention and he couldn't get to him. It was a times like this that he really considered going back to earth. He could have had a surgery position at the University of Glasgow by now if he'd stayed on earth, but here he was stuck in another galaxy worrying over his most frequent patient; who was in yet another life threatening situation. The problem with Colonel Sheppard was, when he got injured, it was very rarely his fault. He'd run a few suicide missions over the years in the name of trying to save lives, but those were few and far between. Situations like the one he was in now came up far too frequently for his liking.

"What am I going to do with you Colonel?" He mumbled to himself.

He was startled from his musings by his radio activating.

He tapped his earpiece. "What have you got Zelenka?"

_Well Carson it was you that gave me the idea, I've found a trap door in the room above the lab, all we need is some ropes to get down to them."_

"Okay Radek let us know how to get there, Carson out."

"_Okay I'm sending Lorne the Coordinates now, Zelenka out."_

Carson suddenly felt apprehensive, as now the hard work would begin; saving the Colonels life, yet again.

**XXXXXXXXXXX**

John was in a constant state of delirium, Rodney couldn't make out what he was saying most of the time, but it wasn't good. His muscles were twitching and convulsing periodically and all Rodney could do was try and keep his friend as cool as possible. The water in his canteen was running out, so he wouldn't be able to keep sponging him down forever. He really needed a miracle right now; not that he believed in miracles.

He was getting up to search for another water source when his radio activated.

"_Rodney it's Carson, Zelenka has found a way in and we'll be there in about twenty minutes, so sit tight."_

"Please hurry Carson? John doesn't look good and I'm running out of water to cool him off with."

"_We'll be there as quickly as we can Rodney, Carson out."_

"See you soon, Rodney out."

He went back over to his friend and started sponging him down again. John started to mutter in his delirium

"Why… is…there…a…dog…licking…me?" He rasped between shallow breaths.

Rodney was becoming increasingly more worried, as he could see that John's breathing was becoming shallower with each passing minute.

"No dog, It's just your best friend Rodney wiping you down with a damp cloth,"

"Why…are…you…doing…that?

"You have a fever John." Rodney said becoming frustrated with the conversation.

"Why….?"

Because you were injected with a drug, okay. It has made you very sick and if Carson doesn't get here soon you're going to die. Do you understand?" He yelled at the sick man.

You've…no….need…to…yell…at…me. I…don't….want…to…die…Rodney." John said, as tears came to his eyes.

"I Know John, just rest Carson will be here soon." Rodney told him in a soothing voice and patted his arm.

"Kay," he said as he lost consciousness again.

As Rodney started wiping John down again, he sent up a silent prayer to a God that he didn't believe in, that this would not be the day that they lost John Sheppard.

**XXXXXXXXXXXXX**

John was floating in the darkness again; there was no light just the constant darkness. Vaguely he heard voices and he strained his ears to listen, but he couldn't work out what they were saying. He thought that he heard Rodney yelling at him and telling him he was going to die.

Tears came to his eyes as he managed to rasp out. "I don't want to die."

He felt a pat on his shoulder and a voice telling him that Carson would be here soon. That gave him hope, so he just lay there in the endless darkness and in his own world of endless pain hoping that it would be soon enough.

**XXXXXXXXXXXXX**

Twenty minutes later Lorne and Carson came upon a corridor. It led to the room with the trapdoor, above the lab the Colonel and Rodney were trapped in. Carson had called for a medical team and a stokes basket along the way. Harris and his team took the lead as they approached the trapdoor.

Harris looked down at the trapdoor looking for a way to open it. He found an iron ring in the centre of it attached to a chain.

"I guess I'll just pull this chain and see what happens then, shall I?" Harris looked around at the rest of the group for conformation.

They all nodded.

Harris pulled as hard as he could and the trapdoor moved, but not by much. Ronan got behind Harris and they both pulled together. Finally it gave and they managed to open it and still stay on their feet.

"Okay I will go first." Harris told them.

"I really need to go first, to check out the Colonel condition!" Carson told him forcefully.

"I _will _go first and then you can follow with your medical supplies, Ronan and Teyla can follow. We'll send the stokes basket after that! "Harris told them equally as forcefully. "Does anyone have any problems with that?" He asked them.

They all shook their heads.

"Will the stokes basket fit through the hole Carson."

"Aye it should do lass."

Carson tapped his earpiece. "Rodney Harris is coming through the trapdoor in the corner of the lab now, I will follow after him."

"_Hurry up Carson he's barley breathing." _

"We'll be there as soon as we can Rodney."

"_Be quick Carson."_

"Aye we will Rodney, Carson out."

**XXXXXXXXXXXXX**

Rodney had run out of water by the time Harris arrived, followed by Carson a few seconds later. Carson ran over to his patient with his medical bag and started taking his vitals.

"Breathing shallow," he said as he placed his stethoscope to John's chest.

"Pulse thready and heart rate low. He's bordering on bradycardia." He explained to his medical team.

"I need that basket over here ASAP?" Carson yelled across the room to Ronan and Teyla.

Ronan and Teyla picked up their pace and they headed over to Carson.

Teyla noticed Rodney standing of to the side staring at what was going on. "How are you Rodney?" She asked him in her usual soothing tone.

"How do you think I am? My best friend is going to die, because of what some ancient; who John is obviously descended from was a criminal. Can you believe it; he is going to die because of something that happened ten thousand years ago?

It was Carson who answered him. "Rodney, he's not going to die, not if I have anything to do with it. I can keep him alive, but I need you to look through the ancient data base and find the antidote for this drug, but first I want you to have a meal and four hours solid sleep. Zelenka can work on finding the antidote until then."

Rodney was about to complain when Teyla took his arm and led him to the trapdoor.

"Carson I will look after Rodney. You just look after John."

A ladder had been placed under the trapdoor, so Teyla let Rodney climb up first and then she followed behind.

"Ronan can you help me get John in the basket please?" Carson asked the big man.

He leant down an picked John up and placed him in the basket. As Ronan placed John in the basket he started to moan in pain.

"Car… son…, is…. that…you…? I can't…see…you." John rasped out in between shallow breaths

"Aye son I'm here, were going to get you out of here as soon as we can." Carson told him and grabbed his hand.

John gave Carson's hand a weak squeeze and drifted back into unconsciousness again.

"Okay let's get him out of here?" Carson began to bark orders.

Ronan picked up one side of the basket while Lorne picked up the other side and Carson came at the head. They walked across to the trap door and attached the ropes that were hanging there to several points around the basket.

When the ropes were attached, Carson yelled up to the combat engineers at the top to start pulling.

Once he was sure that the Basket had reached the top he climbed the ladder and followed. His medical team came next.

Carson climbed out of the hole and started barking orders. "Set up and IV, we'll need to get a cooling blanket on him as soon as we reach the infirmary. Is the scanner ready? I'll need to see what condition his kidney's and liver are in as soon as we reach the infirmary.

He leant down to check his breathing and muttered to himself. "Dam it he's stopped breathing."

**TBC…**

**Sorry about the evil cliff-hanger.**

**I'm always interested to hear what people think, so please review?**


	4. Chapter 4:A mad dash for survival

**Chapter 4: A Mad dash for survival.**

_Carson climbed out of the hole and started barking orders. "Set up an IV, we'll need to get a cooling blanket on him as soon as we reach the infirmary. Is the scanner ready? I'll need to see what condition his kidney's and liver are in as soon as we reach the infirmary."_

_He leant down to check for John's breathing and muttered to himself. "Dam it he's stopped breathing."_

Carson looked up at his staff and started yelling orders again, "somebody bag him, we're going to have to intubate as soon as we get him to the infirmary. Ronan lift him on to the gurney please?"

Ronan lifted John on to the gurney and then he held on to one side of the gurney to assist with the mad dash to get to the infirmary.

One of the medics was pumping air into his starving lungs along the way.

When they reached the infirmary Carson laid John's head back and inserted a laryngoscope into John's mouth and expertly slid a tube down his throat and hooked him up to the ventilator.

While Marie was checking his vitals again Carson was making notes on a chart.

"What's his temperature Marie?" Carson asked.

"104, his blood pressure is 90 over 60 and he's bradycardic." Marie told him.

"I can't really give him too much medication until we know what the drug is in his system." Carson muttered. "Okay, let's get him to the scanner; I want to see how much damage there is to his internal organs." He told his team and started moving the gurney across to the scanner.

Placing the bed under the scanner he ran it over the Colonel's body. Carson was not happy by what he saw.

"His kidneys are failing; we'll need to start him on dialysis. Let's get him into the ICU stat."

Once John was settled into the ICU Carson hooked up the dialysis machine and put a cooling blanket on him to try and lower his temperature. He then flashed his penlight into John's eyes; no response.

"I need to know what the cloudy film is over his eyes. Marie, please make a note of that and get Rodney or Dr Zelenka, to research it in the ancient data base?"

"Yes Doctor." Marie replied.

Finally Carson sat down next to his unconscious patient, he was sickly pale, the tremors had died down and the ventilator and dialysis machine were the only things keeping him alive. He looked at him and mumbled. "Lad what have you gotten yourself into this time?"

**XXXXXXXXXXXXX**

Elizabeth was beside herself with worry by the time she reached to waiting room of the infirmary. Teyla was sitting in the corner in quiet meditation, but Rodney and Ronan were pacing frantically.

"If this Tobias guy wasn't already dead I'd kill him!" Ronan shouted as he through a cushion across the room.

"Calm down Conan, Carson is doing all he can for now. Once Carson tells us what's going on I'm going straight to my lab to find the antidote. Radek has already started looking through the data base for answers." Rodney told him all the while continuing to pace.

"Rodney weren't you supposed to be sleeping?" Elizabeth asked.

"I have told him the same thing Elizabeth, but he doesn't want to listen." Teyla told her softly.

"How can I sleep when John could be dead at this very minute?"

"He's not dead, not yet anyway." Carson told them as he entered the room.

"How is he Carson?" Elizabeth asked the worry evident in her eyes.

They all gathered around Carson to hear the news.

"Not good, he's hooked up to the ventilator, as his lungs aren't working at the moment, he's in complete renal failure, so we've got him on dialysis and there's some kind of cloudy film over his eyes that is preventing him from seeing. All we can do for now, is to make him as comfortable as possible."

He turned and looked at Rodney. "Now Rodney I need you to get some sleep. You'll be no good to John if you collapse. Go directly to your quarters or I will sedate you and keep you here. No arguments please, as I need to get back to my patient."

"Can we sit with him?" Elizabeth asked.

"Yes, but only one person at a time as my medical staff will need space to move around the room."

"You may go first Elizabeth and then we will make up a schedule, so that he is never alone." Teyla told her.

"Thank you Teyla."

"Teyla can you please make sure that Rodney gets to his quarters?" Carson asked.

"Please come with me Rodney?" Teyla took hold of Rodney's arm and led him out of the room.

"I'll go with them to see if she needs help." Ronan told them and then left the room.

Carson turned and looked at Elizabeth, "Okay Lassie come with me?" He said as he led her down the corridor towards the ICU.

When she reached John's bedside she gasped at what she saw, the man lying in the bed was beyond pale and there were all sorts of wires attached to his body. All that could be heard in the room was the whoosh of the ventilator, as it breathed for him.

Carson had taking the bandages off his hands too give them a proper chance to heal. This made it easy for Elizabeth to sit down and hold his hand. She spoke soothing words to him. "John its Elizabeth, your team and I are all here for you, just hang on a little longer and we'll be able to fix this. I need you John; I can't really run this place without you. I don't want to run this place without you. You have to get better."

As she spoke to him he turned his head to the side and his eyelids flickered. She thought he was going to wake, but then nothing.

**XXXXXXXXXXXXX**

All John could remember was floating on a sea of darkness. He couldn't remember a time when there was light. Laying there in the darkness he noticed one thing; the pain had gone and he felt totally numb. That's a good thing he thought, but then the thought struck him. What happened to me, why am I in this dark place and shouldn't I be in pain?

In the midst of the darkness he heard a soft voice, he recognised it, but he couldn't figure out where. Turning towards the lovely voice he tried to open his eyes, but they just wouldn't open. He stopped when he realised there was something down his throat. He thought about trying to remove it, but it just seemed too hard. Laying in the darkness everything started to fade, as his awareness slowly slipped away, he wondered if he would ever wake up again.

**XXXXXXXXXXXXXX**

Two hours later Rodney was back in his lab.

"Shouldn't you still be sleeping?" Zelenka asked him, while rubbing his hands through his already unruly hair.

"There's too much to do to sleep." Rodney told him.

Zelenka walked over to the coffee pot and offered Rodney a cup.

"Thanks, now what have you found?" Rodney asked him.

"Well it seems that only certain ancients had access to the ZPM lab, as they were developing an even more effective ZPM at the time and they didn't want the wraith to find out about the improvements. That is why your DNA was unknown. Tobias was one of the main scientists on the project, but apparently he was handing information to the Wraith."

"Why doesn't the data base say anything about this new and more effective ZedPM?" Rodney asked him curiously.

Well for some reason all evidence of the experiments were erased when the ancients left for earth. I guess they didn't want the information to fall into enemy hands." Zelenka told him, while shifting his glasses back onto his nose.

"Well that's all fascinating, but have you found out any information about the drug Sheppard was injected with or if there is an antidote?" Rodney asked him impatiently. "Or, what about the cloudy film over his eyes?"

"No, it appears that particular information is classified and encrypted. It's going to take a while to gain access to it." Zelenka replied, running his fingers through his hair again, so it looked even messier than John's did.

"Well let's get to it then and you'd better keep the coffee coming, as I think it's going to be a very long day and an even longer night." Rodney just looked at him and sighed.

With that Zelenka walked over to the recently filled coffee pot and poured two cups of steaming hot coffee.

**XXXXXXXXXXXXX**

Teyla wandered into the Carson's office to find him looking at John's charts.

"How is he doing Doctor Beckett?"

"No change, he's alive for now and that's all that matters."

"Can I see him please Carson?"

"Yes by all means luv, Elizabeth left a few minutes ago to go and get something to eat."

Teyla thanked him and headed to John's bedside. He looked even paler than he had the last time that she had seen him and there was sweat glistening on his brow and his usually unruly hair was plastered to his forehead. She sat down next to him and took his hand and noticed it was incredibly cold, despite his obvious fever.

"Carson," she called out.

"Yes luv, is something wrong?" He asked, as he came running.

"Is John supposed to be this cold?" She asked, while rubbing his hand.

"His heart rate is just a wee bit slow at the moment. It's much better than it was though."

"I'll just be in my office, maybe I'll take a wee nap. "He told her, walking away.

Sitting down next to John's bed again, she started to rub his hand and hum a traditional Athosion lullaby, hoping that it would sooth him somehow.

Carson was sitting in his office when Teyla started to hum. He suspected that Teyla and John had deep feelings for one another; feelings that neither one of them would ever act upon, because they never wanted to destroy the friendship they had. Their love really showed through at times like this and Carson wondered if they would ever get their act together and admit their true feelings to one another.

Lying down on his cot in the corner of his office, he decided that it was time to try and get some much needed rest. Closing his eyes he drifted off to sleep.

**XXXXXXXXXXXXX**

After spending an hour trying to sleep, Elizabeth gave up and headed to Rodney's lab. Rodney and Radek both had their noses stuck in the computers, they were typing with one hand and they had a cup of coffee in the other.

"Have you found out anything?" She asked them, taking a seat at Rodney's desk.

"We've found plenty, just nothing to help Sheppard." Rodney told her, getting a little frustrated with the data base.

"Rodney, look at this?" Zelenka called to him from behind his computer.

"Wow that looks interesting," Rodney said looking down at the computer screen.

"Do you think?" Zelenka asked Rodney.

"It's possible Radek."

"Shall we tell Carson?" Radek asked.

"Definitely." Rodney told him.

Elizabeth just stared at them both. "Gentlemen, you do realise neither one of you has completed a sentence. Can you please tell me what's going on?"

"Well, we've finally found the code for the encrypted files, which contain the information about the drug Sheppard was injected with and its antidote. We should be able to access the files in the next thirty minutes or so." Rodney spoke with a huge grin on his face.

He tapped his earpiece, "McKay to Beckett".

"_Yes Rodney" Carson answered back groggily._

"Have you been sleeping Carson, should you be sleeping at a time like this? Is John okay?"

"_Stop ranting Rodney, I just closed my eyes for a few minutes and no, John isn't okay, but he is stable for now. Now what can I do for you Rodney?"_

"We've found the code to break the encrypted files, with information on the drug John was injected with."

"_That's good news, how long will it be before you can give me the antidote? I can't keep him alive by artificial means indefinitely."_

"Could you put him in stasis?" Rodney asked, a little scared at the answer he might hear.

"_If you can't come up with something in the next twenty four hours, I am left with two options. One, take him of life support and let nature take its course or put him stasis to give us a bit longer."_

"Okay Carson I'm on it, Rodney out."

"_Keep me informed, Carson out."_

Rodney looked around at Radek and Elizabeth and told them, "We have twenty four hours to find a solution, so let's get to work."

"Anyone for more coffee, I'll put on a fresh pot." Elizabeth asked.

They nodded at her as she went over to the cupboard where Rodney kept his secret stash of coffee beans.

"Hey how did you know about that?" Rodney asked with a stunned look on his face.

"John told me."

"How did he know?" He asked Elizabeth,

"You'll just have to ask him when he wakes up."

"What if he never wakes up Elizabeth?"

"He will Rodney, he always does." She told him patting his hand and smiling at him.

"Yes of course, I'd better get back to work then." Rodney told her feeling a little bit uncomfortable by the physical touch.

"Just let me know what you find?" She said to both men as she left the lab.

**XXXXXXXXXXXXXXX**

Teyla was holding John's hand and had fallen fast asleep leaning on the side of his bed. All of a sudden the monitors around the bed started to shrill in a high pitched whine. She was startled awake and got up and moved away from the bed, just as Carson came running. Looking down at the bed she saw that John was starting to convulse, his back was arching up of the bed and the whole bed rail was starting to shake, as he thrashed about. Carson held on to his head to make sure that the breathing tube wasn't knocked out of his throat. Marie and the other nurses made sure that none of the other wires were pulled out.

"Can't we give him something for it?" Marie yelled out.

"No as I still don't know how anything is going to interact with the drug he was given. There are still traces of it in his system." Carson told her while still trying to hold John's head still.

Eventually the Convulsions stopped and John relaxed. Carson went about checking his vitals and the ventilator tube and wiring to make sure everything was still connected.

At that moment Carson's radio activated.

"_Carson its Rodney here, apparently the way the drug is supposed to work is that a person falls asleep quietly and then finally slips into a coma and dies forty to forty eight hours later. We think that Sheppard must have had an allergic reaction to the drug, that's why he has been in so much pain. Anyway I need to find the antidote before he slips into a coma, because according to my research at that point, it's too late."_

"Well then Rodney, It's already too late, because he slipped into a coma a few minutes ago."

**TBC…**

**Sorry another evil cliff hanger.**


	5. Chapter 5: Will John Survive?

**Warning: This chapter is really sad, so make sure you have your tissues ready.**

**Chapter 5: Will John Survive?**

Rodney looked up from his computer, his face beaming.

"Hey Radek, I've managed to get in to the files, I know what the drug does; now I have to find the antidote."

"You have to contact Carson straight away." Radek told him.

Rodney tapped his earpiece and spoke.

"Carson its Rodney here, apparently the way the drug is supposed to work is that a person falls asleep quietly and then finally slips into a coma and dies forty to forty eight hours later. We think that Sheppard must have had an allergic reaction to the drug, that's why he has been in so much pain. Anyway I need to find the antidote before he slips into a coma, because according to my research at that point, it's too late."

"_Well then Rodney, It's already too late, because he slipped into a coma a few minutes ago."_

"What are you talking about Carson? He can't have."

"_I'm sorry Rodney, but it's true. There is nothing I can do for him, unless we put him in stasis and I know that goes against John's wishes."_

"Carson I know that there must be an answer, give me the next thirty hours to come up with something. If we can't find something by then we'll have talk about what to do next."

"_Okay you have thirty hours, Carson out."_

"I'll keep you informed, Rodney out."

Rodney looked at Zelenka with tears in his eyes. "Radek John has slipped into a coma, Carson has given us thirty hours to come up with a solution, if we don't by then, well I don't know what will happen to him. He'll most likely die."

"I will go and get us something to eat and you start working." Radek told him, patting his arm as he turned to walk out of the lab.

"How can you eat at a time like this? There is no time. _We need to work!_ Rodney practically yelled at him.

"Remember you have to eat because of you hypoglycaemia," Radek told him softly.

"Okay," Rodney turned to look back at his computer before he spoke again, "and thanks Radek."

"You're welcome Rodney." Radek replied as he walked out of the lab heading towards the mess hall.

**XXXXXXXXXXXXX**

Elizabeth walked in to Carson's office, only to find a distraught Teyla already sitting there. Carson had called an emergency meeting five minutes earlier.

"Teyla what has happened?"

Before Teyla had a chance to reply Ronan walked into the room, "Hey what's up?" He asked.

"I think I will wait for Carson to fill you in." Teyla told them, with unshed tears in her eyes.

Ronan saw that she was upset, sat next to her and put his arms around her. It was all too much for her and she let the tears fall.

"Carson what has happened? Is John dead?" Elizabeth asked with fear in her eyes, as Carson walked into the room.

"No lassie, he's still with us for the moment, but he has slipped into a coma."

"Will he wake up?" Elizabeth asked, fighting back tears.

"I honestly don't know luv, but it doesn't look good. Rodney has found the information on the drug that John was injected with. Apparently the last stage before death is that the patient slips into a coma. They usually die forty to forty-eight hours after that."

Carson was just about in tears himself, by the time he had finished his speech. He knew all about emotional detachment. It was one of the first things they taught you in medical school, but out here in the Pegasus galaxy it was easier said than done. They depended on each other, they were a family and John Sheppard was a big part of that family. John Sheppard had saved all their lives more times than he could count, but he'd also saved John's life on many occasions. That's what made the next thing he had to say even more difficult.

"In John's will he has stated that he doesn't want to be kept alive by artificial means for any more than a week, which means stasis isn't an option. If Rodney can't find a cure in the next two days we're going to have to let him go." Carson told them, and finally let the tears fall.

"Oh no." Elizabeth whispered, as her unshed tears finally started to fall.

Ronan just shouted and walked out of Carson's office heading for the gym, he really needed to punch something.

The rest of them all sat holding each other until their tears subsided.

"What now?" Elizabeth asked.

"Can we sit with him?" Teyla asked.

"Yes, by all means sit and talk to him. Some people believe that people can sense those around them when they're in a coma. I don't really know what to believe, but maybe it's time to think about saying your goodbyes."

"Elizabeth you can go into see John. I really need to get some sleep; I will come back in two hours." Teyla told her, with tears still streaming down her face.

Elizabeth went and sat by John's bed, held his hand and softly whispered in his ear. "John I'm here for you for as long as you need me to be. Teyla will be back shortly and Rodney is still trying to figure this out, so don't give up on us now, because we're not giving up on you."

She sat there holding his hand and talking quietly for another hour until she fell asleep.

**XXXXXXXXXXXXX**

Ronan left the infirmary and ran straight to the gym. Anyone that was in his way was pushed aside; he was frantic by the time he arrived. He looked around for someone to spar with and noticed that the place was deserted.

Stepping up to the punching bag, he thought strongly about hitting it without gloves on, but thought better of it when he realised that Carson had enough to deal with right now, without him busting up his hands.

He looked around and found some gloves to put on, once they were on he started punching and kicking the bag. Yelling and screaming seemed to help too.

Finally exhausted he just sat on the floor, thinking about the man who had become closer than a brother. What would he do if John died, would he even bother to stay in Atlantis? The people here had been wonderful and excepting of him, but it was John who had given him a home and a family. After Sateda was destroyed and he was on the run from the wraith, he thought that he would never have a family again, until he met John. He had captured John and Teyla and tied them up the first time he had met them, but John had still been willing to help him. He could never repay that act of kindness to the man who had become his brother. Finally he headed back to the infirmary to sit with John for what may be the last time.

**XXXXXXXXXXXXX**

Teyla entered the infirmary three hours later to find Ronan sitting in a chair at the end of John's bed; he had his feet on the bed as usual.

"Do you mind if I have a moment alone with him Ronan?"

"Sure I'll just run to the mess hall. Do you want anything?"

"No thankyou I am fine."

Teyla sat next to the bed and took John's hand. She looked at him not really knowing what she could say to him.

Sitting there for a few minutes she finally had the courage to tell him what she had wanted to say to him for a long time.

"John I love you. I've loved you from the moment you entered my tent, that first day you came to Athos, your leader looked right through me, but you did not. You told me of things that I didn't understand and then you told me you loved a good cup of tea. When you flashed that crooked grin at me, I knew that you would be a big part of my future. Please hold on, Rodney is working on a cure. I can't imagine my life without you. You have to get better.

When she had finished talking to him Ronan came in, pulling up a seat beside her, he put his arm around her shoulders and pulled her in for a hug.

Carson came in a few minutes later to check John's vitals.

"How is he Doc?" Ronan asked.

"About the same, without a cure there's nothing I can do now." Carson explained.

"So, we just wait then?" Ronan asked.

"I'm afraid so." Carson told him and then pulled up a seat on the other side of John's bed and held his other hand.

They all sat there in silence thinking about all the fun times they'd had with John.

**XXXXXXXXXXXXX**

Rodney and Zelenka spent hours staring at their computer screens. The answer had to be there, but it seemed to be illusive.

Fifteen hours after the deadline had been decided, Rodney just through his hands up in the air and started ranting.

"Radek we're never going to find anything, it's too late, John is going to die and it's entirely my fault! If I hadn't talked him into exploring that lab this never would have happened. Did you know that he threatened to stun me? If he'd done that this never would have happened. What am I going to do if he dies? Tell me what am I going to do?" There were unshed tears in Rodney's eyes.

Zelenka guided Rodney too his seat and spoke quietly to him, "Rodney why don't you go and sit with him for a while? I can handle things here."

"Are you sure, Radek?"

"Yes I am sure. I've actually managed to have a break and some sleep over the last twenty four hours, you haven't."

"Okay, but please don't stop looking, we only have fifteen hours left."

"Do not worry Rodney I will not stop."

Radek sat down at his computer, as Rodney left the room. I hope we can find something soon or this place will never be the same again, he thought.

**XXXXXXXXXXXXX**

Rodney entered the ICU and found that Carson was sitting with John. He was fast asleep curled up in a chair. Not wanting to disturb Carson, he went around to the other side of the bed and took John's hand. Sitting down he started to talk to him.

"I'm sorry John, I never meant for this to happen. I talked you into exploring the lab and I know you didn't want too. I should have just let you stun me and then you wouldn't be lying there about to die, because I can't find a cure. I'm not giving up though, I'm just going to sit here with you for a while and then I'm going to get back to work. Did I ever tell you that you're my best friend? You always accepted me for who I was and I am so grateful for that. You gave me a chance to get out of the lab and have an interesting life. Thank you for everything you've done for me John. I'll never forget it."

He rested his head on the side of John's bed, still holding John's hand. That's how Carson found him an hour later.

**XXXXXXXXXXXXX**

Radek continued to work long after Rodney had left the lab.

Five hours later he came across a file that was marked antidotes and cures, for lethal drugs. It was encrypted of course, but what surprised him the most was that it was compiled by Tobias Sheppard.

He tapped his earpiece, "Zelenka to McKay, come in."

"_Yes Radek, what have you got?" Rodney replied groggily_

"I've found an encrypted file that is labelled antidotes and cures for lethal drugs."

"_Okay I'm on my way, McKay out."_

"See you in a few minutes, Zelenka out."

Zelenka got to work on trying to break the encryption code on the file. Five minutes later Rodney showed up.

"Okay let me have look?" Rodney said, looking over Zelenka's shoulder.

"Here I'll move." Zelenka told him, generously moving aside.

"Radek this is going to be so easy to break, we should have an answer in an hour or so."

"That's fantastic Rodney."

"Rodney did you happen to see who compiled this list?"

"Yes, the mysterious Tobias Sheppard. That's a mystery for another time."

"I have another question to ask you Rodney?"

"Go ahead; I may not listen though because I'm very busy."

"Why did the hologram believe that John was Tobias, surely the computer would have picked up the differences in their DNA."

"Just another mystery Radek, that isn't really important at this time, maybe the computer was malfunctioning or something."

An hour later Rodney exclaimed loudly, "Finally I have it!"

**XXXXXXXXXXXXX**

The whole team was sitting in the ICU when Rodney's call came through.

"_McKay to Beckett, come in?"_

"Aye Rodney I'm here, what have you got?"

"_We've found the antidote; I'm sending it to your computer now. I'm also sending the file to the chemist's lab, so they can synthesise the compound."_

"That's fantastic news Rodney. Will it work now he's in a coma?"

"_Yes apparently this antidote was formulated sometime after the original one and there's more, apparently blindness is a common side effect of the drug, so Tobias developed a way to cure the blindness. I'm sending you and the chemist's research on that as well."_

"Did you say Tobias?"

"_Yes, he thought that the use of this drug was inhumane, as over seventy percent of people who were exposed to it had an allergic reaction, and died slowly and painfully. This file was harder to find than many of the others. I think that he wanted to keep it secret for some reason. Anyway I think I'll do some research on Tobias later and try to find out what really went on. I'm on my way to the infirmary now, Rodney out."_

"See you soon, Carson out."

Carson looked around at the others, who were staring at him.

"Well are you going to tell us why you have that big grin on your face Carson?" Teyla asked suspiciously.

"Rodney has found the antidote and the chemists are synthesising it now."

A cheer went up around the room, as they all hugged each other; they had hope for the first time in days. Rodney entered the ICU at that point and joined in the hugs.

Trying to calm everyone down, Carson spoke as loudly as he felt comfortable, seeing that this was an ICU.

"Okay, quieten down. This is still an infirmary. Now I want everyone to get a hot meal and five hours sleep."

Rodney was about to protest when Carson continued, "I will let you know if there is any change. I don't want to see any of you back her for six hours. Do you understand?"

"Yes Doctor Beckett. I will go and see John and then I will follow your orders." Teyla told him.

Ronan just grunted and Rodney just walked away.

"I'll head off now and I'll see you later." Elizabeth told him.

Six hours later, Carson was sitting all alone by John's bedside. He looked at him, held his hand and spoke to him.

"Ach laddie, you're lucky this time, it seems the man who was accused of the crimes you're being punished for, has come up with the cure to save your life. Rodney's going to research him a wee bit more when you're feeling better. I'm glad you're going to get better, because this place just wouldn't be the same without you."

Three hours later; nine hours after the file had been sent the chemists lab, everyone was sitting around John's bed, when Dr Paul entered the ICU with the antidote.

Dr Paul spoke quietly to Carson and everyone else strained to listen. "This is the only dose he will need. It varies on how long it takes to work, but he should definitely be okay. We have also synthesised the eye cream to restore his eyesight. That cure should take a few days to work though.

"Good luck," he said as he turned and left the room.

Carson walked over and injected the medication into John's IV Port.

"What now?" Rodney asked.

"Now we wait," Carson replied.

TBC…

**Hopefully John is on the mend now.**


	6. Chapter 6: Explanations

**Chapter 6: Explanations.**

The forty eight hour deadline came and went but still John remained in a coma. Carson was hopeful, as his vitals were steadily improving. Elizabeth and the rest of John's team had come and gone over the last couple of days, but there was always someone there with him holding his hand and speaking words of encouragement and comfort.

It was the third day after the deadline, when John opened his eyes; Rodney was there, when John started to gag on the intubation tube. The monitors and alarms started to wail and Carson came running.

"Carson, what the hell is going on? He's choking to death." Rodney panicked.

"It's okay Rodney; it's a simple reaction to having the ventilator breathing for him." Carson told him as he injected something in to his IV. "I'm going to keep him sedated until we can take him off the ventilator. The good news is that we can do that in the next couple of days."

"Does that mean he's out of a coma?" Rodney asked.

"Ay it does. I should be able to take him off dialysis in the next couple of days as well. When he wakes up and is feeling a wee bit stronger, I'll apply the treatment to his eyes as well."

"That's great, now that I know he's getting better I think I'll go to my lab and do some research on Tobias. Teyla should be here in a few minutes anyway." Rodney told Carson, with a huge grin.

"Okay I'll see you later Rodney."

"Bye Carson."

**XXXXXXXXXXXXX**

John was slowly becoming aware again and he realised that he was still floating in the never ending darkness. What's happened this time he thought to himself? Why, am I here and why am I still in pain? These are all very good questions he thought. Sighing he realised that the only way he could find out was to try and open his eyes. Somehow after struggling for a while he managed the feat, only to find that it was still pitch black and worse than that, there was something stuck down his throat, he tried to breathe, but couldn't because of the obstruction down his throat. He started to gag and then just as he thought he was going to suffocate, a cool numbing liquid began to flow through his veins, he sighed with relief and let the ever encroaching darkness claim him again.

**XXXXXXXXXXXXX**

Forty eight hours later Rodney entered the mess hall, he looked around to see that his whole team; minus John of course, were there, along with Elizabeth and Carson. They hadn't had the chance to eat together for over a week, so it was good the finally get together for a meal.

John had been taken of the ventilator this morning and dialysis the evening before. Things were certainly looking up, John was still unconscious, but his body was healing well. Carson had told them that he should wake up soon and the only side effects of his ordeal would be some lingering weakness for a few weeks; particularly in his limbs.

Rodney filled his tray and headed to the table overlooking the ocean, to join his friends.

"If you're all here, who's sitting with Sheppard?" Rodney asked, looking around the table.

"Major Lorne is with him Rodney; you do not need to worry." Teyla soothed him.

"Why are you here Doctor, you're chief medical officer and the best Doctor in two galaxies, shouldn't you be with John?" Rodney asked, panicking.

Before Carson had a chance to answer Ronan interrupted. "Who are you, and what have you done with McKay?"

Everyone started to laugh at that comment, it was the first time they had laughed in quite a while and it felt good.

"Oh, ha ha," Rodney replied, sarcastically.

"Dr Cole is in the ICU with him, I have every confidence in her abilities and thank you for the complement." Carson told Rodney.

"Well, don't let it go to your head or anything." Rodney told him, grinning from ear to ear.

"Are you going to sit down Rodney?" Elizabeth asked, patting the seat next to her.

"Okay, so what's everyone talking about?" Rodney asked, sitting down next to Elizabeth.

"We were discussing a party for John when he is fully recovered." Teyla told him.

"You do know that he doesn't really like parties?" Rodney asked the group.

"Yes, Rodney we are well aware of his aversion to social gatherings." Teyla told him, rolling her eyes.

"We were thinking sharing a meal together and afterwards watching one of his favourite movies. We were thinking of 'Back to the future.'" Elizabeth told him.

"I hate that movie." Rodney grumbled.

"We're, not watching it for you McKay." Ronan told him forcefully.

Sensing and argument Elizabeth changed the subject. "Have you found out anything more about Tobias?"

"Yes I have. It turns out that someone was sharing advanced ZPM research and technology with the wraith. They believed Tobias was involved, but they could never prove it. I'm guessing someone didn't like him for some reason and decided to use him as a scape goat."

"Who would do that?" Teyla asked.

"I don't know, possibly the person who was collaborating with the wraith."

"So you're saying that it could have been someone on the ruling council, who wanted to cover up their own illegal activities?" Elizabeth asked him.

"It's possible; I wouldn't have a clue why someone would give such advanced technology to the wraith though? Maybe they were part wraith? I guess we'll never know."

"Why did the Computer think that Colonel Sheppard was Tobias? There DNA should be different enough for the computer to recognise that they're two different people." Carson asked him.

"It turns out that Tobias had a son and the traitor wanted him eliminated as well. It was programmed to detect any DNA that was a familial match to his. Obviously John's DNA was a close enough match to be mistaken for Tobias'."

"Well speaking of John I must get back to the infirmary. It was lovely to have lunch with you all." Carson told them as he got up and left.

"Well I must be going too, as I have a mountain of paperwork to catch up on." She told them, waving as she left.

The other three sat their laughing and joking for a while longer. They were just happy to be with each other, knowing that John was going to be ok.

**XXXXXXXXXXXXX**

John was lying there in the darkness, when he heard voices. I know those voices he thought. He tried to open his eyes, but his eyelids were droopy, finally he managed to open them a slit, but the darkness was still there. He started to panic, why couldn't he see, what was happening to him?

He forced out a croak hoping someone would hear him. "Wha…?"

A soothing voice spoke to him. "John it is Teyla, you are in the infirmary and you are going to be okay. I will go and get Carson to explain things to you." She patted his arm as she left the room.

"Kay…" He slurred, not realising that Teyla had left the room.

A few minutes later Carson started to speak to him. "How are you feeling son, would you like some ice chips?"

"Sure." He felt the spoon in his mouth and felt the ice slip down his throat, it was pure heaven.

"Can't….see." His heart rate started to rise, as he started to panic.

Carson gently took John's face in his hands and spoke softly, "John, It's only temporary; we will be able to restore your sight."

It took him a while to calm down. When he was finally able to get his breathing under control, he asked, "Wha… happened to… mee?" He cringed as his speech was still slightly slurred. "And why does… my… throat feel so dry? "

"What do you remember?" Carson asked him.

Turning his head to the sound of Carson's voice, he tried to put in to words what he could remember.

"Rodney and I found and ancient lab, it was full of ZPM's as far as the eye could see. I remember walking in to another lab and being enveloped by a strange blue light. It's a little fuzzy after that, there was a hologram and I remember hearing the name Tobias Sheppard. There was a sharp pain in my arm and then nothing. There were times I was conscious and I remember an incredible pain that came and went. Was there a dog in that lab? I could swear there was a dog licking me at some stage."

"No lad that was Rodney sponging you down, you had a very high fever."

"Okay, Doc why does my throat feel so dry and what's with the feeding tube and cannula? I assume there's a catheter too?"

"Sorry lad, but you were in a coma for four days."

"Why?"

"The drug you were injected with was meant to kill you; it seems that the ancients weren't opposed to capital punishment. It seems that someone framed Tobias Sheppard for handing over ZPM research and technology to the wraith and they were determined that he or his son should die. That's why the computer mistook you for Tobias, it detected a familial match."

"What did the drug do to me?" He asked Carson, beginning to feel weary again.

"Well it was supposed to shut down a person's body slowly and painlessly, but you had an allergic reaction to the drug, which caused your blindness and a great amount of pain. Your lungs gave up rather quickly and we had to intubate."

"Why did you bother, if you knew I was going to die?"

"We knew there was an antidote, Rodney and Radek just needed time to find it, and it seems that Tobias developed the antidote, because he thought that the use of the drug was inhumane. According to Rodney's research seventy percent of people injected had an allergic reaction similar to yours. Tobias also came up with a treatment for the blindness."

"When will I be able to see again Doc?"

"I'll start the treatment in a day or two, when you're feeling stronger. It should restore your sight within two days."

John sensed something in Carson's voice and asked him. "What aren't you telling me Doc?"

"The treatment is only seventy percent effective."

"Great so I may lose my eyesight, because of someone who held a grudge against one of my ancestors over ten thousand years ago?"

"I'm sorry lad."

John closed his eyes, trying to hide the tears that were forming in them, "I want to go back to sleep now."

"I will stay with you John." Teyla told him whispering in his ear.

"I'd rather be alone." He told her rolling over to face away from her.

"If that is what you want." She leant over and kissed his cheek and left the room.

He closed his eyes and fell into a dreamless sleep.

**XXXXXXXXXXXXX**

It was two days later that he woke again feeling much stronger than he had the last time. He laid there with his eyes closed trying to ascertain who was in the room with him. The tapping of the keys gave it away.

He turned his head towards the sound and spoke, "_McKay,_ did you bring me my stunner?"

"Oh I see you're awake and feeling a little bit cranky."

"Of course I'm cranky; I can't see and I've got tubes attached to my body in all sorts of uncomfortable places, all because of you, so at the risk of sounding repetitive. Did _you_ bring me _my_ stunner?"

"Carson said that he'd take the feeding tube out later if you managed to eat something."

"Oh that makes me feel so much better!" He told him, his voice dripping with sarcasm.

"Carson said that I can take you for a walk later if you use a wheelchair."

"Rodney, get out of here and leave me alone, before I hit you."

Rodney was leaving the room just as Carson entered. "Don't go in there if you want to keep your head."

Carson looked at Rodney and then entered the room.

John just yelled at him. "_Rodney_ I told you to get the _hell out of here_!"

"Well someone's in a bad mood today." Carson spoke trying to be light-hearted.

"What do you want Doctor Beckett?" He asked, trying to control his anger.

Carson knew he was in trouble when John called him Doctor Beckett. "I just brought you some lunch."

"How the hell am I supposed to eat that, _I can't see_ or have you forgotten that little detail! And before you ask I don't want any help, I'd rather _not eat_ than be treated like an _invalid_!"

"Okay I'll leave you alone again, but you're going to have to deal with this at some stage." Carson told him preparing to leave the room.

He sighed and spoke in the direction of the door, "Carson, please come back? I'm sorry for shouting at you. This is just a really crappy situation."

"Don't be too hard on Rodney; he blames himself for what happened to you."

"Why? It wasn't his fault; he wasn't the idiot who wanted this Tobias put to death."

"Deep down he knows that, but he did convince you to go into that lab with him."

"You know Carson, Rodney is one of my closest friends, I wouldn't have gone with him if I hadn't wanted to."

"Maybe you should tell him that."

"I know I need to apologise to him."

"Okay now that is settled, do you want to try some broth or not?" Carson asked him.

"No thanks Doc, I really don't feel hungry right now."

"No problems, I'll have to leave the feeding tube in for a few more days though, because tomorrow I want to start the treatment on your eyes. I'll give you a local anaesthetic around your eyes, so there shouldn't be any pain."

"Thanks Doc, I'm feeling really sleepy, I think I'll go back to sleep now."

"Sleep well my friend." Carson whispered as he left the room.

**XXXXXXXXXXXXX**

It was another twenty four hours before he woke again and he knew Rodney was there, because he could hear him tapping on the keyboard.

"Hey, Rodney." He croaked out, still groggy from his sleep.

"John, You're awake how are you feeling?" Rodney realised that maybe he shouldn't have asked him that and tried to back pedal. "Ahh sorry I didn't mean to ask you that."

"I'm feeling much better today, thanks for asking. Can I have some water?"

Rodney held a glass of water with a straw to John's lips. "Thanks, Rodney and I'm sorry for being so angry with you yesterday, this is a really frustrating situation I'm in."

"I'm sorry too John, I should never have asked you to go down to that lab with me."

"It's not your fault Rodney and that's the end of it. Okay?"

"Okay." Rodney replied.

"So, McKay, what's Zelenka been up too, has he ruined any of your experiments lately?"

"No, he's been really helpful, do you think he's been taken over by an alien entity or something."

John just laughed, for the first time since he'd woken up and he felt so much better for it.

Carson came in a few minutes later wondering what was going on.

"I see your feeling much better today lad."

"Much better, thanks Doc," John told him.

Carson looked at Rodney and told him. "You'll need to leave now, because we need to get Colonel Sheppard ready for his procedure."

"See you later, Sheppard and good luck." Rodney told him.

"Thanks McKay."

Twenty minutes later John was lying flat on his back with clamps holding his eyes open. Carson injected the local anaesthetic just below his cheek bones. Ten minutes later his whole face felt numb. Carson stood close to his ear and explained what was going to happen.

"I'm going to spread this cream over your eyes and then we'll bandage your eyes up for twelve hours. Then we'll check the progress. Do you have any questions?"

John shook his head.

"Okay, I'm going to start with your left eye."

He lay as still as he could and soon felt an uncomfortable feeling in his left eye. It was over before he knew it and Carson moved on to his right eye, that was a little more uncomfortable than the left, but he felt no pain. The clamps were then removed quickly.

"Okay let's sit you up," Carson told him, raising his bed. "Can you close your eyes so I can bandage them up?" Carson asked him.

John closed his eyes and leant forward to let Carson bandage his eyes up.

"Okay John all done. We'll check to see how you're going in twelve hours."

"Thanks Doc," John said settling back against his pillows, ready to fall asleep again.

**XXXXXXXXXXXXXX**

During the next twelve hours he had many visitors; not that he really noticed, because he slept most of the time.

Twelve hours later John was having a particularly amusing time with Rodney and Ronan, they were arguing over the amount of food Rodney had eaten for breakfast.

"You ate enough for six people McKay." Ronan Smirked.

"Well I have to keep up my food intake because of my hypoglycaemia and besides you ate enough for ten people." McKay shot back.

John interrupted before it could go any further. "Please guys stop? I have a stitch from laughing."

"What's going on in here?" Carson asked entering the room.

"You don't want to know, Doc." John told him, in between chuckles.

"Okay you two out, so I can check on my patient." Carson grumbled at them.

"See you later Sheppard," Ronan grunted.

"Good luck John," Rodney said to him as he left the room.

"Okay John, I'm going to take the bandages off, when I tell you open your eyes and tell me what you see."

John held his breath as Carson took of the bandages, when Carson told him too he opened his eyes.

"Do you see anything John?"  
"No absolutely nothing, everything is still completely dark."

**TBC…**


	7. Chapter 7: Tobias Sheppard revealed

**Chapter 7: Tobias Sheppard revealed.**

"_Okay John, I'm going to take the bandages off, when I tell you open your eyes and tell me what you see."_

_John held his breath as Carson took of the bandages, when Carson told him too he opened his eyes._

"_Do you see anything John?"_

"_No absolutely nothing, everything is still completely dark."_

John was trying to hold the tears back. What did this mean? Would he now be blind for the rest of his life? Being blind would be the end of his career, the air force would give him an honourable discharge and he would never be able to fly again. They would certainly have no use for a blind ex-pilot on Atlantis. He would lose his home and his family. Maybe he could stay on the mainland with the Athosians, but what use would they have for him. Thinking of this was all too much for his emotions, so he let the tears fall.

Gently Carson tapped him on the shoulder and spoke softly and gently to him. "Don't give up hope lad? The treatment was supposed to take at least forty eight hours to work. Let me bandage your eyes and we'll take another look in twenty four hours' time."

"Thanks Doc." John sat up and let Caron bandage his eyes again, as soon as Carson was finished he lay on his side with his back facing Carson.

"Do you need anything Laddie? Shall I send your team in?"

"No thanks, Carson and I don't want to see anyone right now."

"Okay I'll let them know."

After Carson had left the room John was alone with his thoughts. Why did he even care what happened to Him? He'd turned into a bug, almost had the life sucked out of him by an enormous bug and then to top it off he'd had the life sucked out of him by a wraith. He'd almost died on numerous occasions. Then he almost killed his best friend, what if he'd succeeded?

He thought of Aiden, where was he, was he even alive? He'd let the kid down big time, he should have been able to protect him. What if next time it was Elizabeth or Carson or one of his team? No he'd had enough maybe it was time to head back to earth anyway. As he lay drifting off to sleep, he contemplated whether it was time to hand in his resignation.

**XXXXXXXXXXXXXXX**

When Carson entered the waiting room in the infirmary he saw four faces eagerly looking up at him.

"How is he Carson?" Elizabeth asked him, with a sense of hope in her eyes.

"At this stage there is no improvement, he's still blind."

"Can we see him?" Teyla asked, softly.

"I'm sorry, but he's rather up set and doesn't want to see anyone right now." Carson told them with sadness in his voice.

"But Carson, we're his family; we should be with him right now." Teyla told him, trying to understand what was happening.

"I'm sorry luv maybe, you can see him tomorrow." Carson told her, with understanding in his voice.

"Okay I think I'll head to my quarters for a rest." Elizabeth told them.

The others all agreed that it was probably a good idea to have a rest. They all left the infirmary with their heads hanging low, hoping that tomorrow would be a better day for all of them.

**XXXXXXXXXXXXX**

Two hours after Rodney left the infirmary he was back in his lab. He had to do something to help Sheppard. Sitting down at his computer, he opened up Tobias' files. There must be something here he thought.

Ten minutes later Zelenka walked in. "I heard about Colonel Sheppard. How are you doing?"

"Not good Radek, I have to do something to help him. I don't know what will happen to him if we can't restore his sight. They'd send him back to earth; he'd lose his home and his family." Rodney stated in a high pitched voice.

"Rodney, sit down, I'll get some coffee and I'll give you a hand."

Rodney looked at the littlie scientist with gratitude. "Thanks Radek."

They sat down together poring over the data base and drinking their coffee.

Twenty minutes later Rodney started clicking his fingers ferociously.

"Have you found something Rodney?"

Yes, yes, yes. It seems that the first treatment for the blindness didn't always work, so Tobias developed a course of eye drops and this was always one hundred percent successful. I must tell Carson."

"Rodney it's five am, why don't you wait a few hours and let people get some rest?"

"Great idea Radek, I think I'll go back to bed myself. Goodnight." He said, leaving the room.

Zelenka just smiled and followed him out of the room.

**XXXXXXXXXXXXX**

John was lying in his bed lost in his own thoughts when he heard someone enter the room.

Rolling over on to his back, he greeted them, "Hello Elizabeth."

"How did you know it was me John?"

"I can smell your perfume. You always wear the same one and it smells like flowers."

"I didn't realise that you noticed things like that."

"I didn't until I became blind." He turned his head in her direction and continued on, "Elizabeth I've been thinking, even if my sight is restored, I will be handing in my resignation and heading back to earth. I've really had enough of this almost dying thing and for what? The wraith are still terrorising the Galaxy and there's always some new bad guy out there wanting to kill us."

"John we will discuss this _when_, your eyesight is restored!"

"I'm not changing my mind Elizabeth."

"We'll see. Now why don't you try and get some sleep, I'll stay right here with you."

"Thanks Elizabeth," he told her and drifted off to sleep.

Carson had overheard most of the conversation between Elizabeth and John from the doorway to the room. What would happen to John back on earth? As far as he knew he didn't have any family back there. They had to convince him to stay on Atlantis, no matter what happened. He was deep in thought when his radio activated.

"_Carson it's Rodney." _Rodney seemed very happy for some reason.

"What have you found Rodney?"

"_I've been looking through Tobias' files again and I've found another treatment for the blindness. It seems that because the first one didn't always work, he felt he needed to develop another one. It's the same compound as before, but it is administered in drop form and this one is one hundred percent effective. I'm sending you the files now."_

"Okay Rodney, I'm taking the bandages off in about twelve hours, we'll see what we need to do then, Carson out_." _

Carson walked into John's room to find Elizabeth still sitting beside John's bed. "Is he asleep?"

"No he's isn't," a groggy voice spoke from the bed.

"I have some good news; Rodney has found a new treatment for your eyes in Tobias' files that is one hundred percent successful."

"Wow, for a guy who was supposedly collaborating with the Wraith he really had the ancient's welfare at heart." John said with sarcasm in his voice.

"Yes well, Rodney's still researching Tobias and trying to find out what really made him tick." Carson told him.

"What happens next, Carson?" Elizabeth asked, with a sense of hope.

"In twelve hours we take the bandages off and see if there is any improvement. If there isn't we try the drops."

"How long should it be before the drops work?" John asked him, feeling positive for the first time in days.

"The drops are administered over twenty four hours." Carson told him.

"Thanks Carson."

"I'll see you later John," Carson told him as he left the room.

Once Carson had left the room John spoke to Elizabeth. "I'm still thinking of resigning, I may get lucky this time, but next time I could die. What happens if I can't protect you, Carson or the rest of my team?"

"You can't protect everyone one hundred percent of the time and we're not discussing this now okay, we'll talk about it when you're better."

"Okay. Thanks for Everything Elizabeth."

"You're welcome John."

**XXXXXXXXXXXXX**

Twelve hours later John was dozing when Carson entered the infirmary.

When Carson spoke it startled him. "It's time John."

"Now just sit forward and I'll take off the bandages."

John sat forward and Carson began unravelling the bandages from around his head. When he'd finished, he asked John, to open his eyes. When he had opened his eyes John got the shock of his life. He could see, everything was blurry, but he could see.

"What can you see lad?" Carson asked.

"I can see you, you're a bit blurry, but I can see you." There was excitement in his voice.

"That's fantastic news, I'll put in some of the drops we've synthesised and your eyesight should continue to improve with further doses."

"Thanks Doc, can I see my team now?" He asked.

"Aye I'll send them in laddie."

A few minutes later, when his whole team was sitting beside his bed, he took a deep breath and spoke. "Guys it's fantastic that I can see and I will gain my sight completely, but I think it's time I headed back to earth. I've almost died a few too many times and I need to re-evaluate my life. When I'm finally out of here, I will be heading back to earth. I've told Elizabeth and when I can see properly I will be sending my resignation to General O'Neill. That is my final decision and I do not wish to discuss it further."

His Team mates just all sat there stunned.

"I do not know what to say." Teyla whispered.

"You can't," Rodney exploded.

I'll kick your ass, if you leave." Ronan grunted.

"Okay guys what's been happening around here since I've been out of commission?" He asked, changing the subject.

"Not much, Radek and I have been desperately trying to save your life and you seem just a little ungrateful for it." Rodney stated, glaring at him.

"If you can't accept my decision, then maybe you'd better leave." He told them all, beginning to sulk.

At that point they all got up to leave. "Goodbye John." Teyla said to him, with tears in her eyes.

Rodney and Ronan just left.

He lay there feeling sorry for himself. He couldn't risk losing anyone else. Not like Mitch or Dax. He had made a promise to himself that he would never get close to anyone again after losing his two best friends, but here he was again having let these people in, but not any longer. He was leaving.

His eye sight improved steadily over the next few days, he'd had plenty of time to think in that time, because no one came to visit him. Carson had tried to talk to him, but he wasn't interested in talking to his team. He'd made his decision and it was final.

Two days after Carson had announced that his eyesight was back to one hundred percent normal; he was finishing up his letter of resignation while eating his lunch, when Rodney entered.

"What can I do for you Dr McKay?" He asked, in a matter of fact tone"

"When I was going through Tobias' files, I found a holographic recording for his son. It is DNA locked, so I suspect that you would be able to open it. I've asked Carson and he's said that I can take you down to the hologram room, if you use the wheelchair."

John looked at him suspiciously, "Why would I want to look at that?"

"It was addressed to his son on his eighteenth birthday. I suspect that he never got to see it and I thought that someone should see it."

John thought that this sounded interesting and nodded his consent. "Okay, I'll come and have a look."

At that moment Teyla came in with a wheelchair. "Do you need help to get in?" She asked with a grin on her face.

"No I'm fine. I have been up a few times in the last few days and I've even managed to go to the bathroom by myself." He said his voice dripping with sarcasm.

He stood up shakily and sat in the wheelchair. Taking the handles Ronan started pushing him down the corridor towards the hologram room. Once inside Rodney set up the recording for him.

"All you have to do is touch this panel and it should play for you." Rodney told him.

"Stay," he said looking at all of them. "Stay and watch with me."

They nodded as John placed his hand on the panel.

A hologram sprang to life. The man was the splitting image of John except for Tobias had red hair; John was glad he'd dodged that bullet. He leaned forward as the man began to speak.

"_Dearest Jason,_

_I am your father Tobias Sheppard._

_At the time of this recording, you are twelve months old. I'm recording this so that when you are older you may understand the reasons why I did what I did. _

_You may have heard many things about me. The main one I think would be that I have been collaborating with the wraith and handing our research on ZPM technology to them._

_Part of this is true I have been working with the wraith, but I have never handed over any of our top secret research or technology._

_I have been involved in a group consisting of both human and wraith scientists, who wish to see peace restored to our galaxy. As a group we have been working towards an end to this war, a solution where both sides can live in harmony as equals._

_We have been working on a way for the wraith to never have to feed on humans. The wraith, have the same digestive system as we have, but eating food through the mouth doesn't sustain them the way it does humans._

_Anyway there are those; a great many at that, who don't believe what we're doing is right._

_I know that you are preparing to leave through the stargate back to earth, but at this time I can't return with you and your mother. I am a wanted man, the ancient council has charged me with treason and if I am captured I will be put to death._

_I want you to know my son, that everything I have done, it was done with the hope that one day our descendants may live in a galaxy at peace. They will never know what it is like to live in constant fear of the wraith._

_It is my hope that as equals, wraith and humans can work together for scientific exploration and discovery._

_I'm sorry that I haven't been there to watch you grow into the incredible young man I'm sure you have become._

_I hope you can understand and forgive me for not sharing your journey with you, but know this I love you and remember, everything I did, I did because I love you and your mother._

_Just try to remember that killing isn't always the answer, sometimes negotiation and collaboration can bring about a positive outcome for everyone._

_I love you Jason, I hope you live a long and fulfilling life."_

They all sat in stunned silence for a moment, before Rodney spoke. "Wow, what an incredible man, he wasn't a traitor, he was a visionary."

John looked around at each of them, his friends, his family, sighing he asked them, "Can I have a moment alone please?"

They nodded and left him sitting alone in the middle of the empty room.

John sat totally stunned at what he had just seen. Rodney had said it, Tobias Sheppard was a visionary, risking everything, for the chance of peace for generations to come and that was his lineage, he was proud of that.

Sitting there thinking of his friends and family on Atlantis, he realised that he was fighting for the same things that Tobias was, he was fighting for peace throughout the galaxy for future generations.

He felt tears welling up in his eyes thinking of Jason Sheppard, did he ever get to see his father again. I guess I'll never know he thought.

He sat there in silence for thirty minutes until Teyla came back in and knelt down next to him. "Are you okay John?"

"Yes Teyla for the first time a long time, I think I am."

"Carson said that we could take you for a walk. Where would you like to go?"

"Take me to my favourite balcony overlooking the ocean and I want you all to come with me."

Teyla walked around behind him and grabbed the back of the chair and pushed him out of the room.

John was happier than he'd been in a while, as they walked through the doors to his favourite balcony.

Standing up and holding onto the railing, he looked over at the ocean feeling the cool breeze in his face, he felt alive.

He looked at Rodney and asked, "Did you ever find out who was handing secrets to the wraith?"

"Apparently it was the leader of the ruling council at the time; he was part wraith and felt more of an affinity with the wraith than the ancients. He didn't want peace; he wanted the wraith to be the superior race in the galaxy. Somehow he found out what Tobias was up to and didn't want a bar of it, so he framed him."

Looking around at his family, John took a deep breath and spoke, "I've decided that I'm not going to resign, I'm going to stay here and fight for peace, the only way I know how. I want to honour the legacy that Tobias' left for those who came after him."

"That's wonderful John." Elizabeth told him joining them on the balcony.

Carson followed a short time later. They all sat around enjoying the sunset, thankful to be alive and to be there with each other.

In the days that followed John became stronger; his recovery was happing much faster now that he had a new lease on life. He'd discovered his purpose in life, thanks to an ancestor from ten thousand years ago.

Over the coming weeks John spent many nights watching movies with his Atlantis family. It was on one such night that he shared a thought with his friends.

"If I ever have a son I'm going to name him Tobias Jason Sheppard or T.J. for short."

**Fin... **

**I hope you enjoyed it. Please review.**


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